Jonathan Shapey

44 papers A 2Journal 32Unranked 10

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	OOD-SEG: Exploiting out-of-distribution detection techniques for learning image segmentation from sparse multi-class positive-only annotations. Medical Image Anal. Junwen Wang, Zhonghao Wang, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren
2025	J	`jnl`	A generalisable head MRI defacing pipeline: Evaluation on 2,566 meningioma scans. CoRR Lorena Garcia-Foncillas Macias, Aaron Kujawa, Aya Elshalakany, Jonathan Shapey, Tom Vercauteren
2025	J	`jnl`	Label tree semantic losses for rich multi-class medical image segmentation. CoRR Junwen Wang, Oscar MacCormac, William Rochford, Aaron Kujawa, Jonathan Shapey, Tom Vercauteren
2025	J	`jnl`	Longitudinal Vestibular Schwannoma Dataset with Consensus-based Human-in-the-loop Annotations. CoRR Navodini Wijethilake, Marina Ivory, Oscar MacCormac, Siddhant Kumar, Aaron Kujawa, Lorena Garcia-Foncillas Macias, Rebecca Burger, Amanda Hitchings, Suki Thomson, Sinan Barazi, Eleni Maratos, Rupert Obholzer, Dan Jiang, Fiona McClenaghan, Kazumi Chia, Omar Al-Salihi, Nick Thomas, Steve Connor, Tom Vercauteren, Jonathan Shapey
2025	—	`conf`	ReCAP: Recursive Cross Attention Network for Pseudo-label Generation in Robotic Surgical Skill Assessment. Agentic AI/CREATE/Clinical MLLMs@MICCAI Julien Quarez, Marc Modat, Sébastien Ourselin, Jonathan Shapey, Alejandro Granados
2025	J	`jnl`	Systematic Review of Pituitary Gland and Pituitary Adenoma Automatic Segmentation Techniques in Magnetic Resonance Imaging. CoRR Mubaraq Yakubu, Navodini Wijethilake, Jonathan Shapey, Andrew P. King, Alexander Hammers
2025	J	`jnl`	Themed Challenges to Solve Data Scarcity in Africa: A Proposition for Increasing Local Data Collection and Integration. CoRR Mubaraq Yakubu, Udunna Anazodo, Maruf Adewole, Theodore Barfoot, Tiarna Lee, Tom Vercauteren, Jonathan Shapey, Andrew P. King, Alexander Hammers
2025	—	`conf`	Tree-Based Semantic Losses: Application to Sparsely-Supervised Large Multi-class Hyperspectral Segmentation. MICCAI (8) Junwen Wang, Oscar MacCormac, William Rochford, Aaron Kujawa, Jonathan Shapey, Tom Vercauteren
2025	J	`jnl`	Tree-based Semantic Losses: Application to Sparsely-supervised Large Multi-class Hyperspectral Segmentation. CoRR Junwen Wang, Oscar MacCormac, William Rochford, Aaron Kujawa, Jonathan Shapey, Tom Vercauteren
2025	J	`jnl`	UltraFlwr - An Efficient Federated Medical and Surgical Object Detection Framework. CoRR Yang Li, Soumya Snigdha Kundu, Maxence Boels, Toktam Mahmoodi, Sébastien Ourselin, Tom Vercauteren, Prokar Dasgupta, Jonathan Shapey, Alejandro Granados
2025	A	`conf`	Vine4Spine: A Steerable Tip-Growing Robot with Contact Force Estimation for Navigation in the Spinal Subarachnoid Space. IROS Zicong Wu, S. M. Hadi Sadati, Panagiotis Vartholomeos, Mohamed E. M. K. Abdelaziz, Burak Temelkuran, George Petrou, Thomas C. Booth, Jonathan Shapey, Aminul Ahmed, Christos Bergeles
2025	J	`jnl`	X-RAFT: Cross-Modal Non-Rigid Registration of Blue and White Light Neurosurgical Hyperspectral Images. CoRR Charlie Budd, Silvère Ségaud, Matthew Elliot, Graeme Stasiuk, Yijing Xie, Jonathan Shapey, Tom Vercauteren
2025	—	`conf`	X-RAFT: Cross-Modal Non-rigid Registration of Blue and White Light Neurosurgical Hyperspectral Images. COLAS@MICCAI Charlie Budd, Silvère Ségaud, Matthew Elliot, Graeme Stasiuk, Yijing Xie, Jonathan Shapey, Tom Vercauteren
2025	J	`jnl`	crossMoDA Challenge: Evolution of Cross-Modality Domain Adaptation Techniques for Vestibular Schwannoma and Cochlea Segmentation from 2021 to 2023. CoRR Navodini Wijethilake, Reuben Dorent, Marina Ivory, Aaron Kujawa, Stefan Cornelissen, Patrick Langenhuizen, Mohamed Okasha, Anna Oviedova, Hexin Dong, Bogyeong Kang, Guillaume Sallé, Luyi Han, Ziyuan Zhao, Han Liu, Tao Yang, Shahad Hardan, Hussain Alasmawi, Santosh Sanjeev, Yuzhou Zhuang, Satoshi Kondo, Maria G. Baldeon Calisto, Shaikh Muhammad Uzair Noman, Cancan Chen, Ipek Oguz, Rongguo Zhang, Mina Rezaei, Susana K. Lai-Yuen, Satoshi Kasai, Chih-Cheng Hung, Mohammad Yaqub, Lisheng Wang, Benoit M. Dawant, Cuntai Guan, Ritse Mann, Vincent Jaouen, Ji-Wung Han, Li Zhang, Jonathan Shapey, Tom Vercauteren
2024	A	`conf`	A self-supervised and adversarial approach to hyperspectral demosaicking and RGB reconstruction in surgical imaging. BMVC Peichao Li, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren
2024	J	`jnl`	A self-supervised and adversarial approach to hyperspectral demosaicking and RGB reconstruction in surgical imaging. CoRR Peichao Li, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren
2024	—	`conf`	Blood Harmonisation of Endoscopic Transsphenoidal Surgical Video Frames on Phantom Models. ISBI Mahrukh Saeed, Julien Quarez, Hassna Irzan, Bava Kesavan, Matthew Elliot, Oscar MacCormac, James Knight, Sébastien Ourselin, Jonathan Shapey, Alejandro Granados
2024	J	`jnl`	Brain Tumor Segmentation (BraTS) Challenge 2024: Meningioma Radiotherapy Planning Automated Segmentation. CoRR Dominic LaBella, Katherine Schumacher, Michael Mix, Kevin Leu, Shan McBurney-Lin, Pierre Nedelec, Javier E. Villanueva-Meyer, Jonathan Shapey, Tom Vercauteren, Kazumi Chia, Omar Al-Salihi, Justin Leu, Lia Halasz, Yury Velichko, Chunhao Wang, John Kirkpatrick, Scott Floyd, Zachary J. Reitman, Trey Mullikin, Ulas Bagci, Sean Sachdev, Jona A. Hattangadi-Gluth, Tyler M. Seibert, Nikdokht Farid, Connor Puett, Matthew W. Pease, Kevin Shiue, Syed Muhammad Anwar, Shahriar Faghani, Muhammad Ammar Haider, Pranav I. Warman, Jake Albrecht, András Jakab, Mana Moassefi, Verena Chung, Alejandro Aristizabal, Alexandros Karargyris, Hasan Kassem, Sarthak Pati, Micah J. Sheller, Christina Huang, Aaron Coley, Siddharth Ghanta, Alex Schneider, Conrad Sharp, Rachit Saluja, Florian Kofler, Philipp Lohmann, Philipp Vollmuth, Louis Gagnon, Maruf Adewole, Hongwei Bran Li, Anahita Fathi Kazerooni, Nourel Hoda Tahon, Udunna Anazodo, Ahmed W. Moawad, Bjoern H. Menze, Marius George Linguraru, Mariam Aboian, Benedikt Wiestler, Ujjwal Baid, Gian Marco Conte, Andreas M. Rauschecker, Ayman Nada, Aly H. Abayazeed, Raymond Y. Huang, Maria Correia de Verdier, Jeffrey D. Rudie, Spyridon Bakas, Evan Calabrese
2024	J	`jnl`	Deep learning for automatic segmentation of vestibular schwannoma: a retrospective study from multi-center routine MRI. Frontiers Comput. Neurosci. Aaron Kujawa, Reuben Dorent, Steve Connor, Suki Thomson, Marina Ivory, Ali Vahedi, Emily Guilhem, Navodini Wijethilake, Robert Bradford, Neil Kitchen, Sotirios Bisdas, Sébastien Ourselin, Tom Vercauteren, Jonathan Shapey
2024	—	`conf`	MUTUAL: Towards Holistic Sensing and Inference in the Operating Room. ISIC/iMIMIC/EARTH/DeCaF@MICCAI Julien Quarez, Yang Li, Hassna Irzan, Matthew Elliot, Oscar MacCormac, James Knigth, Martin Huber, Toktam Mahmoodi, Prokar Dasgupta, Sébastien Ourselin, Nicholas Raison, Jonathan Shapey, Alejandro Granados
2024	J	`jnl`	OOD-SEG: Out-Of-Distribution detection for image SEGmentation with sparse multi-class positive-only annotations. CoRR Junwen Wang, Zhonghao Wang, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren
2024	J	`jnl`	R-Trans - A Recurrent Transformer Model for Clinical Feedback in Surgical Skill Assessment. CoRR Julien Quarez, Matthew Elliot, Oscar MacCormac, Nawal Khan, Marc Modat, Sébastien Ourselin, Jonathan Shapey, Alejandro Granados
2024	J	`jnl`	Scribble-Based Interactive Segmentation of Medical Hyperspectral Images. CoRR Zhonghao Wang, Junwen Wang, Charlie Budd, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren
2023	J	`jnl`	A Clinical Guideline Driven Automated Linear Feature Extraction for Vestibular Schwannoma. CoRR Navodini Wijethilake, Steve Connor, Anna Oviedova, Rebecca Burger, Tom Vercauteren, Jonathan Shapey
2023	J	`jnl`	CrossMoDA 2021 challenge: Benchmark of cross-modality domain adaptation techniques for vestibular schwannoma and cochlea segmentation. Medical Image Anal. Reuben Dorent, Aaron Kujawa, Marina Ivory, Spyridon Bakas, Nicola Rieke, Samuel Joutard, Ben Glocker, M. Jorge Cardoso, Marc Modat, Kayhan Batmanghelich, Arseniy Belkov, Maria G. Baldeon Calisto, Jae Won Choi, Benoit M. Dawant, Hexin Dong, Sergio Escalera, Yubo Fan, Lasse Hansen, Mattias P. Heinrich, Smriti Joshi, Victoriya Kashtanova, Hyeongyu Kim, Satoshi Kondo, Christian N. Kruse, Susana K. Lai-Yuen, Hao Li, Han Liu, Buntheng Ly, Ipek Oguz, Hyungseob Shin, Boris Shirokikh, Zixian Su, Guotai Wang, Jianghao Wu, Yanwu Xu, Kai Yao, Li Zhang, Sébastien Ourselin, Jonathan Shapey, Tom Vercauteren
2023	—	`conf`	Deep Reinforcement Learning Based System for Intraoperative Hyperspectral Video Autofocusing. MICCAI (9) Charlie Budd, Jianrong Qiu, Oscar MacCormac, Martin Huber, Christopher E. Mower, Mirek Janatka, Théo Trotouin, Jonathan Shapey, Mads S. Bergholt, Tom Vercauteren
2023	J	`jnl`	Deep Reinforcement Learning Based System for Intraoperative Hyperspectral Video Autofocusing. CoRR Charlie Budd, Jianrong Qiu, Oscar MacCormac, Martin Huber, Christopher E. Mower, Mirek Janatka, Théo Trotouin, Jonathan Shapey, Mads S. Bergholt, Tom Vercauteren
2023	J	`jnl`	MedShapeNet - A Large-Scale Dataset of 3D Medical Shapes for Computer Vision. CoRR Jianning Li, Antonio Pepe, Christina Gsaxner, Gijs Luijten, Yuan Jin, Narmada Ambigapathy, Enrico Nasca, Naida Solak, Gian Marco Melito, Afaque R. Memon, Xiaojun Chen, Jan Stefan Kirschke, Ezequiel de la Rosa, Patrick Ferdinand Christ, Hongwei Bran Li, David G. Ellis, Michele R. Aizenberg, Sergios Gatidis, Thomas Küstner, Nadya Shusharina, Nicholas Heller, Vincent Andrearczyk, Adrien Depeursinge, Mathieu Hatt, Anjany Sekuboyina, Maximilian Löffler, Hans Liebl, Reuben Dorent, Tom Vercauteren, Jonathan Shapey, Aaron Kujawa, Stefan Cornelissen, Patrick Langenhuizen, Achraf Ben-Hamadou, Ahmed Rekik, Sergi Pujades, Edmond Boyer, Federico Bolelli, Costantino Grana, Luca Lumetti, Hamidreza Salehi, Jun Ma, Yao Zhang, Ramtin Gharleghi, Susann Beier, Arcot Sowmya, Eduardo A. Garza-Villarreal, Thania Balducci, et al.
2023	J	`jnl`	Spatial gradient consistency for unsupervised learning of hyperspectral demosaicking: Application to surgical imaging. CoRR Peichao Li, Muhammad Asad, Conor C. Horgan, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren
2023	J	`jnl`	Spatial gradient consistency for unsupervised learning of hyperspectral demosaicking: application to surgical imaging. Int. J. Comput. Assist. Radiol. Surg. Peichao Li, Muhammad Asad, Conor C. Horgan, Oscar MacCormac, Jonathan Shapey, Tom Vercauteren
2023	J	`jnl`	TISS-net: Brain tumor image synthesis and segmentation using cascaded dual-task networks and error-prediction consistency. Neurocomputing Jianghao Wu, Dong Guo, Lu Wang, Shuojue Yang, Yuanjie Zheng, Jonathan Shapey, Tom Vercauteren, Sotirios Bisdas, Robert Bradford, Shakeel R. Saeed, Neil Kitchen, Sébastien Ourselin, Shaoting Zhang, Guotai Wang
2022	—	`conf`	Boundary Distance Loss for Intra-/Extra-meatal Segmentation of Vestibular Schwannoma. MLCN@MICCAI Navodini Wijethilake, Aaron Kujawa, Reuben Dorent, Muhammad Asad, Anna Oviedova, Tom Vercauteren, Jonathan Shapey
2022	J	`jnl`	Boundary Distance Loss for Intra-/Extra-meatal Segmentation of Vestibular Schwannoma. CoRR Navodini Wijethilake, Aaron Kujawa, Reuben Dorent, Muhammad Asad, Anna Oviedova, Tom Vercauteren, Jonathan Shapey
2022	J	`jnl`	CrossMoDA 2021 challenge: Benchmark of Cross-Modality Domain Adaptation techniques for Vestibular Schwnannoma and Cochlea Segmentation. CoRR Reuben Dorent, Aaron Kujawa, Marina Ivory, Spyridon Bakas, Nicola Rieke, Samuel Joutard, Ben Glocker, Jorge Cardoso, Marc Modat, Kayhan Batmanghelich, Arseniy Belkov, Maria G. Baldeon Calisto, Jae Won Choi, Benoit M. Dawant, Hexin Dong, Sergio Escalera, Yubo Fan, Lasse Hansen, Mattias P. Heinrich, Smriti Joshi, Victoriya Kashtanova, Hyeongyu Kim, Satoshi Kondo, Christian N. Kruse, Susana K. Lai-Yuen, Hao Li, Han Liu, Buntheng Ly, Ipek Oguz, Hyungseob Shin, Boris Shirokikh, Zixian Su, Guotai Wang, Jianghao Wu, Yanwu Xu, Kai Yao, Li Zhang, Sébastien Ourselin, Jonathan Shapey, Tom Vercauteren
2022	J	`jnl`	Deep learning approach for hyperspectral image demosaicking, spectral correction and high-resolution RGB reconstruction. Comput. methods Biomech. Biomed. Eng. Imaging Vis. Peichao Li, Michael Ebner, Philip J. Noonan, Conor C. Horgan, Anisha Bahl, Sébastien Ourselin, Jonathan Shapey, Tom Vercauteren
2021	J	`jnl`	Deep Learning Approach for Hyperspectral Image Demosaicking, Spectral Correction and High-resolution RGB Reconstruction. CoRR Peichao Li, Michael Ebner, Philip J. Noonan, Conor C. Horgan, Anisha Bahl, Sébastien Ourselin, Jonathan Shapey, Tom Vercauteren
2021	J	`jnl`	Integrated multi-modality image-guided navigation for neurosurgery: open-source software platform using state-of-the-art clinical hardware. Int. J. Comput. Assist. Radiol. Surg. Jonathan Shapey, Thomas Dowrick, Rémi Delaunay, Eleanor C. Mackle, Stephen A. Thompson, Mirek Janatka, Roland Guichard, Anastasis Georgoulas, David Pérez-Suárez, Robert Bradford, Shakeel R. Saeed, Sébastien Ourselin, Matthew J. Clarkson, Tom Vercauteren
2021	—	`conf`	Inter Extreme Points Geodesics for End-to-End Weakly Supervised Image Segmentation. MICCAI (2) Reuben Dorent, Samuel Joutard, Jonathan Shapey, Aaron Kujawa, Marc Modat, Sébastien Ourselin, Tom Vercauteren
2021	J	`jnl`	Inter Extreme Points Geodesics for Weakly Supervised Segmentation. CoRR Reuben Dorent, Samuel Joutard, Jonathan Shapey, Aaron Kujawa, Marc Modat, Sébastien Ourselin, Tom Vercauteren
2020	J	`jnl`	Manual segmentation versus semi-automated segmentation for quantifying vestibular schwannoma volume on MRI. Int. J. Comput. Assist. Radiol. Surg. Hari McGrath, Peichao Li, Reuben Dorent, Robert Bradford, Shakeel R. Saeed, Sotirios Bisdas, Sébastien Ourselin, Jonathan Shapey, Tom Vercauteren
2020	—	`conf`	Scribble-Based Domain Adaptation via Co-segmentation. MICCAI (1) Reuben Dorent, Samuel Joutard, Jonathan Shapey, Sotirios Bisdas, Neil Kitchen, Robert Bradford, Shakeel R. Saeed, Marc Modat, Sébastien Ourselin, Tom Vercauteren
2020	J	`jnl`	Scribble-based Domain Adaptation via Co-segmentation. CoRR Reuben Dorent, Samuel Joutard, Jonathan Shapey, Sotirios Bisdas, Neil Kitchen, Robert Bradford, Shakeel R. Saeed, Marc Modat, Sébastien Ourselin, Tom Vercauteren
2019	—	`conf`	Automatic Segmentation of Vestibular Schwannoma from T2-Weighted MRI by Deep Spatial Attention with Hardness-Weighted Loss. MICCAI (2) Guotai Wang, Jonathan Shapey, Wenqi Li, Reuben Dorent, Alex Demitriadis, Sotirios Bisdas, Ian Paddick, Robert Bradford, Shaoting Zhang, Sébastien Ourselin, Tom Vercauteren
2019	J	`jnl`	Automatic Segmentation of Vestibular Schwannoma from T2-Weighted MRI by Deep Spatial Attention with Hardness-Weighted Loss. CoRR Guotai Wang, Jonathan Shapey, Wenqi Li, Reuben Dorent, Alex Demitriadis, Sotirios Bisdas, Ian Paddick, Robert Bradford, Sébastien Ourselin, Tom Vercauteren